Controllable lossy compression of BAM/CRAM files
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
keepbed:file
BED file defining regions to keep quality
bedout:boolean
set to true to output suspicious regions to a BED file
bam
*.bam:file
optional filtered/compressed BAM file
*.{bam}
cram
*.cram:file
optional filtered/compressed CRAM file
*.{cram}
sam
*.sam:file
optional filtered/compressed SAM file
*.{sam}
bed
*.bed:file
optional suspicious regions BED file
*{bed}
versions
versions.yml:file
File containing software versions
versions.yml
